FDIC also announced civil fines of $110,000 for Higher One and $172,000 for Bancorp Bank.

Higher One’s president, Miles Lasater, said in an interview Wednesday that the restitution was made in 2011 and that the company changed the way it was collecting fees in 2010, after it learned those fees were not proper under FDIC rules.

The actual amount repaid was $4.7 million, not $11 million, Lasater said, because the lower amount was the total collected improperly by the company between 2008 and 2010, although $11 million had been assessed.

“Everything in this order has already been worked on and resolved,” said Lasater, a Higher One co-founder. “We communicated with clients about this in 2011.”

The FDIC settlement came amid an action-packed week for Higher One, which offers financial management services to colleges and students.

Higher One said late Tuesday it was buying Buffalo, N.Y.-based Campus Labs, which collects and analyzes data of various kinds at colleges and universities. The deal combines two companies that were founded a dozen years ago by students. Campus Labs will operate separately for the time being, Lasater said. It is on 630 campuses compared with 830 for Higher One.

Higher One, which went public in 2010, has not commented on an Aug. 2 story by Bloomberg News saying the company had hired Goldman Sachs to seek possible buyers. “It’s difficult for us to comment on rumors like that. Our primary goal is to build long-term shareholder value,” Lasater said in the interview.

Higher One Holdings Inc. also said its revenues were up in the second quarter, though net income was down compared with a year earlier. Total revenue in the recent quarter was $38.9 million, up from $35.1 million, a somewhat smaller sales gain than Higher One has seen in recent years Net income was $4.05 million, or 7 cents a diluted share, compared with $4.75 million, or 8 cents, but the 2011 second quarter included a $1.5 million legal settlement. Operating income was up a healthy 32 percent.

Higher One’s board authorized a $100 million share buyback. Shares were trading at $11.20 late Wednesday, down 21 cents. The company went public at $12 in June 2010.

Higher One has about 250 employees in New Haven, where several months ago the firm moved into $46 million quarters in former Winchester Repeating Arms buildings in the Science Park development. In all, the company has about 750 employees, including 90 at Campus Labs.